VAP-mediated membrane tethering mechanisms implicate ER-PM contact function in pH homeostasis

VAMP-associated proteins (VAPs) are highly conserved endoplasmic reticulum (ER) resident proteins that establish ER contacts with multiple membrane compartments in many eukaryotes. However, VAP-mediated membrane tethering mechanisms remain ambiguous. Here, focusing on fission yeast ER-plasma membrane (PM) contact formation, using systematic interactome analyses and quantitative microscopy, we predict a non-VAP-protein direct binding-based tethering mechanism of VAPs. We further demonstrate that VAP-anionic phospholipids interactions underlie ER-PM association and define the pH-responsive nature of VAP-tethered membrane contacts. Importantly, such conserved interactions with anionic phospholipids are generally defective in amyotrophic lateral sclerosis (ALS)-associated human VAPB mutant. Moreover, we identify a conserved FFAT-like motif locating at the autoinhibitory hotspot of the essential PM proton pump Pma1. This modulatory VAP-Pma1 interaction is crucial for pH homeostasis. We thus propose an ingenious strategy for maintaining intracellular pH by coupling Pma1 modulation with pH-sensory ER-PM contacts via VAP-mediated interactions.